ConGen-A Simulator-Agnostic Visual Language for Definition and Generation of Connectivity in Large and Multiscale Neural Networks.
PMID:35069166
Realistic retinal modeling unravels the differential role of excitation and inhibition to starburst amacrine cells in direction selectivity.
PMID:34968385
PymoNNto: A Flexible Modular Toolbox for Designing Brain-Inspired Neural Networks.
PMID:34790108
A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience.
PMID:34709562
Specifications of standards in systems and synthetic biology: status and developments in 2021.
PMID:34674411
The EBRAINS NeuroFeatureExtract: An Online Resource for the Extraction of Neural Activity Features From Electrophysiological Data.
PMID:34512300
Predicting Synaptic Connectivity for Large-Scale Microcircuit Simulations Using Snudda.
PMID:34282528
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.
PMID:34019658
Temporal constrained objects for modelling neuronal dynamics.
PMID:33816812
Accelerating with FlyBrainLab the discovery of the functional logic of the Drosophila brain in the connectomic and synaptomic era.
PMID:33616035
HippoUnit: A software tool for the automated testing and systematic comparison of detailed models of hippocampal neurons based on electrophysiological data.
PMID:33513130
Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits.
PMID:33253147
SBML Level 3: an extensible format for the exchange and reuse of biological models.
PMID:32845085
Specifications of standards in systems and synthetic biology: status and developments in 2020.
PMID:32598316
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE).
PMID:32598315
NeuroConstruct-based implementation of structured-light stimulated retinal circuitry.
PMID:32580768
Editorial: Reproducibility and Rigour in Computational Neuroscience.
PMID:32536859
An open-source framework for neuroscience metadata management applied to digital reconstructions of neuronal morphology.
PMID:32219575
The SONATA data format for efficient description of large-scale network models.
PMID:32092054
Enabling Large-Scale Simulations With the GENESIS Neuronal Simulator.
PMID:31803040
Brian 2, an intuitive and efficient neural simulator.
PMID:31429824
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019.
PMID:31301675
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits.
PMID:31201122
The Design of FluxML: A Universal Modeling Language for 13C Metabolic Flux Analysis.
PMID:31178829
NetPyNE, a tool for data-driven multiscale modeling of brain circuits.
PMID:31025934
Multimodal Modeling of Neural Network Activity: Computing LFP, ECoG, EEG, and MEG Signals With LFPy 2.0.
PMID:30618697
Reproducible Neural Network Simulations: Statistical Methods for Model Validation on the Level of Network Activity Data.
PMID:30618696
Computational neuroscience and neuroinformatics: Recent progress and resources.
PMID:30541962
Web-Based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization.
PMID:30483089
Harmonizing semantic annotations for computational models in biology.
PMID:30462164
Code Generation in Computational Neuroscience: A Review of Tools and Techniques.
PMID:30455637
Replicability or reproducibility? On the replication crisis in computational neuroscience and sharing only relevant detail.
PMID:30377880
OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans.
PMID:30201845
Towards systematic, data-driven validation of a collaborative, multi-scale model of Caenorhabditis elegans.
PMID:30201844
Geppetto: a reusable modular open platform for exploring neuroscience data and models.
PMID:30201843
c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans.
PMID:30201842
Reproducible Research Using Biomodels.
PMID:30191472
Parameter Optimization Using Covariance Matrix Adaptation-Evolutionary Strategy (CMA-ES), an Approach to Investigate Differences in Channel Properties Between Neuron Subtypes.
PMID:30108495
BioNet: A Python interface to NEURON for modeling large-scale networks.
PMID:30071069
FindSim: A Framework for Integrating Neuronal Data and Signaling Models.
PMID:29997492
Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures.
PMID:29765315
Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience.
PMID:29713272
Model-based deconstruction of cortical evoked potentials generated by subthalamic nucleus deep brain stimulation.
PMID:29694280
DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation.
PMID:29599715
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.
PMID:29596055
Modeling sources of interlaboratory variability in electrophysiological properties of mammalian neurons.
PMID:29357465
MAGPIE: Simplifying access and execution of computational models in the life sciences.
PMID:29244826
Recent Advances in the Systems Biology of Aging.
PMID:29020802
Software for Brain Network Simulations: A Comparative Study.
PMID:28775687
Wiring variations that enable and constrain neural computation in a sensory microcircuit.
PMID:28530904
Synaptic input sequence discrimination on behavioral timescales mediated by reaction-diffusion chemistry in dendrites.
PMID:28422010
Reproducibility and Comparability of Computational Models for Astrocyte Calcium Excitability.
PMID:28270761
Methods for Specifying Scientific Data Standards and Modeling Relationships with Applications to Neuroscience.
PMID:27867355
Collection of Simulated Data from a Thalamocortical Network Model.
PMID:27837401
Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience.
PMID:27629590
SpineCreator: a Graphical User Interface for the Creation of Layered Neural Models.
PMID:27628934
Is realistic neuronal modeling realistic?
PMID:27535372
Handling Metadata in a Neurophysiology Laboratory.
PMID:27486397
Modeling the Cerebellar Microcircuit: New Strategies for a Long-Standing Issue.
PMID:27458345
PyRhO: A Multiscale Optogenetics Simulation Platform.
PMID:27148037
Reproducibility in Computational Neuroscience Models and Simulations.
PMID:27046845
Neurokernel: An Open Source Platform for Emulating the Fruit Fly Brain.
PMID:26751378
GeNN: a code generation framework for accelerated brain simulations.
PMID:26740369
The volterra functional series is a viable alternative to kinetic models for synaptic modeling--calibration and benchmarking.
PMID:26736995
Golgi: Interactive Online Brain Mapping.
PMID:26635596
NSDF: Neuroscience Simulation Data Format.
PMID:26585711
NeuroManager: a workflow analysis based simulation management engine for computational neuroscience.
PMID:26528175
Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping.
PMID:26492141
An algorithm to detect and communicate the differences in computational models describing biological systems.
PMID:26490504
The role of markup for enabling interoperability in health informatics.
PMID:26042043
Annotation-based feature extraction from sets of SBML models.
PMID:25904997
ModelView for ModelDB: Online Presentation of Model Structure.
PMID:25896640
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.
PMID:25759811
Combining computational models, semantic annotations and simulation experiments in a graph database.
PMID:25754863
Curve interpolation model for visualising disjointed neural elements.
PMID:25657704
Improving collaboration by standardization efforts in systems biology.
PMID:25538939
BioModels: ten-year anniversary.
PMID:25414348
OpenWorm: an open-science approach to modeling Caenorhabditis elegans.
PMID:25404913
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2.
PMID:25309419
Network structure within the cerebellar input layer enables lossless sparse encoding.
PMID:25123311
A flexible, interactive software tool for fitting the parameters of neuronal models.
PMID:25071540
Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX): comparing multi-electrode recordings from simulated and biological mammalian cortical tissue.
PMID:24863422
libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.
PMID:24795618
Equation-oriented specification of neural models for simulations.
PMID:24550820
morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python.
PMID:24478690
N2A: a computational tool for modeling from neurons to algorithms.
PMID:24478635
LFPy: a tool for biophysical simulation of extracellular potentials generated by detailed model neurons.
PMID:24474916
Current practice in software development for computational neuroscience and how to improve it.
PMID:24465191
Reaction-diffusion in the NEURON simulator.
PMID:24298253
From model specification to simulation of biologically constrained networks of spiking neurons.
PMID:24253973
Action and language mechanisms in the brain: data, models and neuroinformatics.
PMID:24234916
A neuroinformatics of brain modeling and its implementation in the Brain Operation Database BODB.
PMID:24234915
Neural Schematics as a unified formal graphical representation of large-scale Neural Network Structures.
PMID:24167490
Computational models and emergent properties of respiratory neural networks.
PMID:23687564
Supercomputers ready for use as discovery machines for neuroscience.
PMID:23129998
Employing NeuGen 2.0 to automatically generate realistic morphologies of hippocampal neurons and neural networks in 3D.
PMID:23111491
Application of a "staggered walk" algorithm for generating large-scale morphological neuronal networks.
PMID:23056037
TrakEM2 software for neural circuit reconstruction.
PMID:22723842
The layer-oriented approach to declarative languages for biological modeling.
PMID:22615554
The connection-set algebra--a novel formalism for the representation of connectivity structure in neuronal network models.
PMID:22437992
Python as a federation tool for GENESIS 3.0.
PMID:22276101
A federated design for a neurobiological simulation engine: the CBI federated software architecture.
PMID:22242154
Channelpedia: an integrative and interactive database for ion channels.
PMID:22232598
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE).
PMID:22180826
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.
PMID:22172142
Software for systems biology: from tools to integrated platforms.
PMID:22048662
Controlled vocabularies and semantics in systems biology.
PMID:22027554
A framework for the study of multiple realizations: the importance of levels of analysis.
PMID:21772823
Modeling signal transduction leading to synaptic plasticity: evaluation and comparison of five models.
PMID:21559300
Stochastic amplification of calcium-activated potassium currents in Ca2+ microdomains.
PMID:21538141
Determinants of synaptic integration and heterogeneity in rebound firing explored with data-driven models of deep cerebellar nucleus cells.
PMID:21052805
Code generation: a strategy for neural network simulators.
PMID:20857234